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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021;595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]

Affiliation(s)

Toni M. Delorey Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Carly G. K. Ziegler Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,3Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA,4Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,5Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,6Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA,7Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
Graham Heimberg Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Rachelly Normand Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,9Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,10Harvard Medical School, Boston, MA 02115, USA,11Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Yiming Yang Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Åsa Segerstolpe Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Domenic Abbondanza Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Stephen J. Fleming Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142,13Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Ayshwarya Subramanian Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Daniel T. Montoro Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Karthik A. Jagadeesh Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Kushal K. Dey Department of Epidemiology, Harvard School of Public Health
Pritha Sen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,15Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,16Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Michal Slyper Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Yered H. Pita-Juárez Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,10Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA,18Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA,19Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Devan Phillips Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jana Biermann Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY,21Columbia Center for Translational Immunology, New York, NY
Zohar Bloom-Ackermann Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Nick Barkas Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
Andrea Ganna Institute for Molecular Medicine Finland, Helsinki, Finland,24Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
James Gomez Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Johannes C. Melms Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY,21Columbia Center for Translational Immunology, New York, NY
Igor Katsyv Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
Erica Normandin Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,10Harvard Medical School, Boston, MA 02115, USA
Pourya Naderi Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA,18Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
Yury V. Popov Harvard Medical School, Boston, MA 02115, USA,26Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,27Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Siddharth S. Raju Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,28Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA,29FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Sebastian Niezen Harvard Medical School, Boston, MA 02115, USA,26Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,27Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Linus T.-Y. Tsai Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,10Harvard Medical School, Boston, MA 02115, USA,26Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,30Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115,31Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Katherine J. Siddle Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,32Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
Malika Sud Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Victoria M. Tran Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Shamsudheen K. Vellarikkal Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,33Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Yiping Wang Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY,21Columbia Center for Translational Immunology, New York, NY
Liat Amir-Zilberstein Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Deepak S. Atri Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,33Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Joseph Beechem NanoString Technologies Inc., Seattle, WA 98109, USA
Olga R. Brook Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Jonathan Chen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,36Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
Prajan Divakar NanoString Technologies Inc., Seattle, WA 98109, USA
Phylicia Dorceus Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jesse M. Engreitz Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,37Department of Genetics and BASE Initiative, Stanford University School of Medicine
Adam Essene Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,30Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115,31Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Donna M. Fitzgerald Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Robin Fropf NanoString Technologies Inc., Seattle, WA 98109, USA
Steven Gazal Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
Joshua Gould Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
John Grzyb Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Tyler Harvey Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jonathan Hecht Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Tyler Hether NanoString Technologies Inc., Seattle, WA 98109, USA
Judit Jané-Valbuena Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Michael Leney-Greene Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Hui Ma Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Cristin McCabe Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Daniel E. McLoughlin Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Eric M. Miller NanoString Technologies Inc., Seattle, WA 98109, USA
Christoph Muus Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,41John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
Mari Niemi Institute for Molecular Medicine Finland, Helsinki, Finland
Robert Padera Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115,42Harvard-MIT Division of Health Sciences and Technology, Cambridge MA,43Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
Liuliu Pan NanoString Technologies Inc., Seattle, WA 98109, USA
Deepti Pant Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,30Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115,31Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Carmel Pe’er Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jenna Pfiffner-Borges Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Christopher J. Pinto Department of Medicine, Harvard Medical School, Boston, MA 02115, USA,38Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Jacob Plaisted Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Jason Reeves NanoString Technologies Inc., Seattle, WA 98109, USA
Marty Ross NanoString Technologies Inc., Seattle, WA 98109, USA
Melissa Rudy Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Erroll H. Rueckert NanoString Technologies Inc., Seattle, WA 98109, USA
Michelle Siciliano Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Alexander Sturm Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Ellen Todres Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Avinash Waghray Harvard Stem Cell Institute, Cambridge, MA, USA,45Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Sarah Warren NanoString Technologies Inc., Seattle, WA 98109, USA
Shuting Zhang Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Daniel R. Zollinger NanoString Technologies Inc., Seattle, WA 98109, USA
Lisa Cosimi Infectious Diseases Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
Rajat M. Gupta Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,33Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Nir Hacohen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,9Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,47Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Hanina Hibshoosh Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
Winston Hide Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA,18Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA,19Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Alkes L. Price Department of Epidemiology, Harvard School of Public Health
Jayaraj Rajagopal Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Purushothama Rao Tata Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
Stefan Riedel Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Gyongyi Szabo Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,10Harvard Medical School, Boston, MA 02115, USA,26Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
Timothy L. Tickle Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,12Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
Patrick T. Ellinor Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA
Deborah Hung Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,50Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,51Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
Pardis C. Sabeti Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,32Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,52Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA,53Howard Hughes Medical Institute, Chevy Chase, MD, USA,54Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
Richard Novak Wyss Institute for Biologically Inspired Engineering, Harvard University
Robert Rogers Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,56Massachusetts General Hospital, MA 02114, USA
Donald E. Ingber John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138,55Wyss Institute for Biologically Inspired Engineering, Harvard University,57Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
Z. Gordon Jiang Harvard Medical School, Boston, MA 02115, USA,26Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA,27Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Dejan Juric Department of Medicine, Harvard Medical School, Boston, MA 02115, USA,38Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Mehrtash Babadi Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142,13Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Samouil L. Farhi Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Benjamin Izar Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY,21Columbia Center for Translational Immunology, New York, NY,58Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY,59Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY
James R. Stone Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
Ioannis S. Vlachos Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,10Harvard Medical School, Boston, MA 02115, USA,17Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA,18Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA,19Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Isaac H. Solomon Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Orr Ashenberg Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Caroline B.M. Porter Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Bo Li Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,16Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Alex K. Shalek Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,3Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA,4Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,5Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,6Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA,7Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA,10Harvard Medical School, Boston, MA 02115, USA,44Harvard Stem Cell Institute, Cambridge, MA, USA,60Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,61Program in Immunology, Harvard Medical School, Boston, MA 02115, USA,62Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Alexandra-Chloé Villani Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,8Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,9Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,16Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Orit Rozenblatt-Rosen Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,63Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
Aviv Regev Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA,5Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,53Howard Hughes Medical Institute, Chevy Chase, MD, USA,63Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA

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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. bioRxiv 2021:2021.02.25.430130. [PMID: 33655247 PMCID: PMC7924267 DOI: 10.1101/2021.02.25.430130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]

Abstract

The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.

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Affiliation(s)

Toni M. Delorey Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Carly G. K. Ziegler Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
Graham Heimberg Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Rachelly Normand Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA Harvard Medical School, Boston, MA 02115, USA Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Yiming Yang Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Asa Segerstolpe Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Domenic Abbondanza Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Stephen J. Fleming Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Ayshwarya Subramanian Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Daniel T. Montoro Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Karthik A. Jagadeesh Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Kushal K. Dey Department of Epidemiology, Harvard School of Public Health
Pritha Sen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Michal Slyper Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Yered H. Pita-Juárez Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Devan Phillips Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Zohar Bloom-Ackerman Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Nick Barkas Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
Andrea Ganna Institute for Molecular Medicine Finland, Helsinki, Finland Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
James Gomez Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Erica Normandin Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA
Pourya Naderi Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
Yury V. Popov Harvard Medical School, Boston, MA 02115, USA Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Siddharth S. Raju Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Sebastian Niezen Harvard Medical School, Boston, MA 02115, USA Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Linus T.-Y. Tsai Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115 Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Katherine J. Siddle Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
Malika Sud Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Victoria M. Tran Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Shamsudheen K. Vellarikkal Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Liat Amir-Zilberstein Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Deepak S. Atri Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Joseph Beechem NanoString Technologies Inc., Seattle, WA 98109, USA
Olga R. Brook Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Jonathan Chen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
Prajan Divakar NanoString Technologies Inc., Seattle, WA 98109, USA
Phylicia Dorceus Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jesse M. Engreitz Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Genetics and BASE Initiative, Stanford University School of Medicine
Adam Essene Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115 Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Donna M. Fitzgerald Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Robin Fropf NanoString Technologies Inc., Seattle, WA 98109, USA
Steven Gazal Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
Joshua Gould Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
John Grzyb Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Tyler Harvey Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jonathan Hecht Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Tyler Hether NanoString Technologies Inc., Seattle, WA 98109, USA
Judit Jane-Valbuena Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Michael Leney-Greene Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Hui Ma Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Cristin McCabe Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Daniel E. McLoughlin Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Eric M. Miller NanoString Technologies Inc., Seattle, WA 98109, USA
Christoph Muus Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
Mari Niemi Institute for Molecular Medicine Finland, Helsinki, Finland
Robert Padera Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 Harvard-MIT Division of Health Sciences and Technology, Cambridge MA Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
Liuliu Pan NanoString Technologies Inc., Seattle, WA 98109, USA
Deepti Pant Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115 Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA
Carmel Pe’er Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Jenna Pfiffner-Borges Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Christopher J. Pinto Department of Medicine, Harvard Medical School, Boston, MA 02115, USA Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Jacob Plaisted Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Jason Reeves NanoString Technologies Inc., Seattle, WA 98109, USA
Marty Ross NanoString Technologies Inc., Seattle, WA 98109, USA
Melissa Rudy Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Erroll H. Rueckert NanoString Technologies Inc., Seattle, WA 98109, USA
Michelle Siciliano Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Alexander Sturm Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Ellen Todres Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Avinash Waghray Harvard Stem Cell Institute, Cambridge, MA, USA Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Sarah Warren NanoString Technologies Inc., Seattle, WA 98109, USA
Shuting Zhang Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Daniel R. Zollinger NanoString Technologies Inc., Seattle, WA 98109, USA
Lisa Cosimi Infectious Diseases Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
Rajat M. Gupta Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
Nir Hacohen Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Winston Hide Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Alkes L. Price Department of Epidemiology, Harvard School of Public Health
Jayaraj Rajagopal Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Purushothama Rao Tata Duke University School of Medicine, Durham, NC
Stefan Riedel Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Gyongyi Szabo Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA
Timothy L. Tickle Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
Deborah Hung Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
Pardis C. Sabeti Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
Richard Novak Wyss Institute for Biologically Inspired Engineering, Harvard University
Robert Rogers Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Massachusetts General Hospital, MA 02114, USA
Donald E. Ingber John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 Wyss Institute for Biologically Inspired Engineering, Harvard University Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
Z. Gordon Jiang Harvard Medical School, Boston, MA 02115, USA Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Dejan Juric Department of Medicine, Harvard Medical School, Boston, MA 02115, USA Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
Mehrtash Babadi Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Samouil L. Farhi Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
James R. Stone Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
Ioannis S. Vlachos Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Isaac H. Solomon Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
Orr Ashenberg Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Caroline B.M. Porter Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA
Bo Li Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Alex K. Shalek Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA Harvard Medical School, Boston, MA 02115, USA Harvard Stem Cell Institute, Cambridge, MA, USA Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Program in Immunology, Harvard Medical School, Boston, MA 02115, USA Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Alexandra-Chloé Villani Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
Orit Rozenblatt-Rosen Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
Aviv Regev Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA

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